From: Richard Wood (
Date: Fri Dec 11 2015 - 08:51:37 CST

One needs to type "E:\VMD\nanotubes-files" and not
"E:/VMD/nanotubes-files". That's one problem.
From: [] on behalf of Ajasja Ljubeti []
Sent: Friday, December 11, 2015 2:31 AM
To: Ashar Malik
Cc: Julio Cantu; VMD Mailing List
Subject: Re: vmd-l: Unable to access config file

Yes, that's a windows "feature". To change drives you have to enter "E:".
Or install Git for windows<> and you will get a fully functional bash shell:)


On 11 December 2015 at 05:57, Ashar Malik <<>> wrote:
As you can see when you do:

C:\Users\Julio>cd E:/VMD/nanotubes-files

your next prompt still reads this


when it should read


in short your attempt at changing path doesn't work. Meaning when you run NAMD, it tries to look for the conf file in the wrong folder and hence fail.

Solution: Make sure you are in the same folder as your conf file before you run NAMD.

On Fri, Dec 11, 2015 at 12:36 PM, Julio Cantu <<>> wrote:

Hello all,

I am attempting to follow the nanotubes tutorial, but have trouble when submitting my own namd job. I receive the following error once I initiate the simulation:

C:\Users\Julio>cd E:/VMD/nanotubes-files

C:\Users\Julio>E:/VMD/NAMD/namd2 sim_short.conf
Charm++: standalone mode (not using charmrun)
Charm++ warning> fences and atomic operations not available in native assembly
Converse/Charm++ Commit ID: v6.6.1-rc1-1-gba7c3c3-namd-charm-6.6.1-build-2014-De
[0] isomalloc.c> Disabling isomalloc because mmap() does not work
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 unique compute nodes (4-way SMP).
Charm++> cpu topology info is gathered in 0.000 seconds.
Info: NAMD 2.10 for Win64-multicore
Info: Please visit
Info: for updates, documentation, and support information.
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info: Based on Charm++/Converse 60601 for multicore-win64
Info: Built Tue, Dec 09, 2014 3:31:31 PM by jim on europa
Info: Running on 1 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0 s
Info: 4.49219 MB of memory in use based on GetProcessMemoryInfo
Info: Configuration file is sim_short.conf
FATAL ERROR: Unable to access config file sim_short.conf
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Unable to access config file sim_short.conf

Charm++ fatal error:
FATAL ERROR: Unable to access config file sim_short.conf

I apologize if the solution if trivial, but if anyone may have some insight as to what I am doing wrong, I would greatly appreciate it.

Thank you for your time and consideration.